Phytozome: a comparative platform for green plant genomics
Identifieur interne : 001077 ( Pmc/Curation ); précédent : 001076; suivant : 001078Phytozome: a comparative platform for green plant genomics
Auteurs : David M. Goodstein [États-Unis] ; Shengqiang Shu [États-Unis] ; Russell Howson [États-Unis] ; Rochak Neupane [États-Unis] ; Richard D. Hayes [États-Unis] ; Joni Fazo [États-Unis] ; Therese Mitros [États-Unis] ; William Dirks [États-Unis] ; Uffe Hellsten [États-Unis] ; Nicholas Putnam [États-Unis] ; Daniel S. Rokhsar [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Abstract
The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (
Url:
DOI: 10.1093/nar/gkr944
PubMed: 22110026
PubMed Central: 3245001
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Goodstein</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr944-AFF1">U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Shu, Shengqiang" sort="Shu, Shengqiang" uniqKey="Shu S" first="Shengqiang" last="Shu">Shengqiang Shu</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr944-AFF1">U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Howson, Russell" sort="Howson, Russell" uniqKey="Howson R" first="Russell" last="Howson">Russell Howson</name><affiliation wicri:level="1"><nlm:aff id="gkr944-AFF1">The Center for Integrative Genomics, University of California, Berkeley, California 94720, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Center for Integrative Genomics, University of California, Berkeley, California 94720</wicri:regionArea></affiliation></author><author><name sortKey="Neupane, Rochak" sort="Neupane, Rochak" uniqKey="Neupane R" first="Rochak" last="Neupane">Rochak Neupane</name><affiliation wicri:level="1"><nlm:aff id="gkr944-AFF1">The Center for Integrative Genomics, University of California, Berkeley, California 94720, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Center for Integrative Genomics, University of California, Berkeley, California 94720</wicri:regionArea></affiliation></author><author><name sortKey="Hayes, Richard D" sort="Hayes, Richard D" uniqKey="Hayes R" first="Richard D." last="Hayes">Richard D. 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Rokhsar</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="gkr944-AFF1">U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>U.S. Department of Energy, Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="gkr944-AFF1">The Center for Integrative Genomics, University of California, Berkeley, California 94720, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Center for Integrative Genomics, University of California, Berkeley, California 94720</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (<ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net">http://www.phytozome.net</ext-link>), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Swarbreck, D" uniqKey="Swarbreck D">D Swarbreck</name></author><author><name sortKey="Wilks, C" uniqKey="Wilks C">C Wilks</name></author><author><name sortKey="Lamesch, P" uniqKey="Lamesch P">P Lamesch</name></author><author><name sortKey="Berardini, Tz" uniqKey="Berardini T">TZ Berardini</name></author><author><name sortKey="Garcia Hernandez, M" uniqKey="Garcia Hernandez M">M Garcia-Hernandez</name></author><author><name sortKey="Foerster, H" uniqKey="Foerster H">H Foerster</name></author><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Meyer, T" uniqKey="Meyer T">T 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article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22110026</article-id><article-id pub-id-type="pmc">3245001</article-id><article-id pub-id-type="doi">10.1093/nar/gkr944</article-id><article-id pub-id-type="publisher-id">gkr944</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>Phytozome: a comparative platform for green plant genomics</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Goodstein</surname><given-names>David M.</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="gkr944-COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Shu</surname><given-names>Shengqiang</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Howson</surname><given-names>Russell</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Neupane</surname><given-names>Rochak</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hayes</surname><given-names>Richard D.</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fazo</surname><given-names>Joni</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mitros</surname><given-names>Therese</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Dirks</surname><given-names>William</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hellsten</surname><given-names>Uffe</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Putnam</surname><given-names>Nicholas </given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rokhsar</surname><given-names>Daniel S.</given-names></name><xref ref-type="aff" rid="gkr944-AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="gkr944-AFF1"><sup>2</sup></xref></contrib></contrib-group><aff id="gkr944-AFF1"><sup>1</sup>U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 and<sup>2</sup>The Center for Integrative Genomics, University of California, Berkeley, California 94720, USA</aff><author-notes><corresp id="gkr944-COR1">*To whom correspondence should be addressed. Tel: <phone>+415 200 6110</phone>; Fax: <fax>+925 927 2552</fax>; E-mail: <email>dmgoodstein@lbl.gov</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>22</day><month>11</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>22</day><month>11</month><year>2011</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>40</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D1178</fpage><lpage>D1186</lpage><history><date date-type="received"><day>7</day><month>9</month><year>2011</year></date><date date-type="accepted"><day>12</day><month>10</month><year>2011</year></date></history><permissions><copyright-statement>Published by Oxford University Press 2011.</copyright-statement><copyright-year>2011</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (<ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net">http://www.phytozome.net</ext-link>), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.</p></abstract><counts><page-count count="9"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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